GLBRC Data Sets

Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation.

A facile spectroscopic method, our CASA (Cysteine–Assisted Sulfuric Acid) method, was developed to quantify the lignin content of lignocellulosic biomass, based on an extraordinary system in which biomass samples are fully dissolved in H2SO4.

Here, we evolved respiration-deficient S. cerevisiae strains that can grow on and ferment xylose to ethanol aerobically, a trait analogous to the Crabtree/Warburg Effect for glucose.

Using Bayesian inference to couple 25 years of in situ N2O flux measurements with site-specific Michaelis–Menten kinetics of nitrification-derived N2O, we test the relative importance of nitrification-derived N2O across six cropped and unmanaged ecosystems along a management intensity gradient in the U.S. Midwest.

Here we use a long-term record of carbon cycling from six paired sites plus a seventh reference site that are all spatially close to each other, with an average of ∼11 km separation. The goal is to use field observations from one of the paired sites, along with observations from the second site that can be measured easily, in order to estimate carbon cycling at the second site using artificial intelligence methods.

Here, we performed time series genome-resolved metatranscriptomics to explore gene expression patterns of coexisting Accumulibacter clades in the same bioreactor ecosystem. Our work provides an approach for elucidating ecologically relevant functions based on gene expression patterns between closely related microbial populations.

We used amplicon sequencing to track switchgrass (Panicum virgatum) LFEs in a greenhouse and field experiment as communities assembled from seed endophytes and rain fungi (integration of wet and dry aerial dispersal) in germinating seeds, seedlings, and adult plants.

Here, we measured fitness costs of over 4000 overexpressed genes in 15 Saccharomyces cerevisiae strains representing different lineages, to explore natural variation in tolerating gene overexpression (OE).

To contribute to the understanding of how plants respond to spaceflight stress, we examined the significance of the unfolded protein response (UPR), a conserved signaling cascade that responds to a number of unfavorable environmental stresses, in the model plant Arabidopsis thaliana.

We grew 725 clonally replicated genotypes of a large full sib family from a four-way linkage mapping population, created from deeply diverged upland and lowland switchgrass ecotypes, at three common gardens.

Here, we describe the isolation of an exceptional lignocellulose-degrading fungus that produces new oxidase activity with no cofactor requirements.

We present a genome-resolved metagenomics data set consisting of 86 metagenome-assembled genome sequences from a photosynthetically operated lab-scale bioreactor simulating EBPR.

The synthetic yield and isolation efficiency of racemic pinoresinol from coniferyl alcohol by conventional radical coupling methods is sub-optimal. In this work, a facile and efficient synthetic approach was developed to synthesize pinoresinol with much higher yield.

Here, we establish machine learning models for predicting whether a gene pair is likely redundant or not in the model plant Arabidopsis thaliana based on six feature categories: functional annotations, evolutionary conservation including duplication patterns and mechanisms, epigenetic marks, protein properties including posttranslational modifications, gene expression, and gene network properties.

To examine poorly resolved relationships and assess progress toward a genome-scale phylogeny of the fungal kingdom, we compiled a phylogenomic data matrix of 290 genes from the genomes of 1,644 species that includes representatives from most major fungal lineages.

By carrying out a phylogenomic analysis of 77 isolates, we find that C. tropicalis genomes range from very homozygous to highly heterozygous. We show that the heterozygous isolates are hybrids, most likely formed by mating between different parents.

We used state- and land cover class-specific accuracy statistics from the USDA from 2008 to 2016 to comprehensively characterize the performance of the CDL across space and time. We estimated nationwide area-weighted accuracies for the CDL for specific crops as well as for the aggregated classes of cropland and non-cropland.

Here, we characterize the 16S rRNA gene diversity and seasonal assembly of bacterial and archaeal microbiomes of two perennial cellulosic feedstocks, switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus x giganteus).

Soils can lose carbon (C) as they dry and, if soil samples vary in moisture content at sampling, differential C loss during the pre-assay dry-down period may complicate the assay’s interpretations. We examined the impact of pre-assay CO2 loss in a long-cultivated agricultural soil at initial moisture contents of 30 %, 50 %, and 70 % water-filled pore space (WFPS).